[gmx-users] g_wham missing option

[Jochen Hub]

Hi Anthony,

just one remark here: Make sure you have always a couple of histograms 
overlapping each other (maybe 5-10). If every histogram overlaps only 
with two neighbors, you will severely underestimate the error.

Hence, to estimate the error, you need rather many histograms from many 
short umbrella simulations than few histograms from few long umbrella 
simulations.

Cheers,
Jochen


Am 2/3/13 11:43 AM, schrieb Nash, Anthony:
> Hi Justin,
>
> Thanks for the reply. You were spot on about the version difference.
>
> Thanks again.
> Anthony
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: 02 February 2013 18:06
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_wham missing option
>
> On 2/2/13 12:58 PM, Nash, Anthony wrote:
>> Hi All,
>>
>> I am using Gromacs 4.5.5 and running free energy calculations. According to the article "g_wham - A Free Weighted Histogram......" (J. Chem. Theory. Comput. 2010, 6, 3713-3720), there is the option -bs-method. However, I am unable to find this option when running g_wham. I want to use bayesian bootstraps of complete histograms.
>>
>> I have a feeling I am missing something completely obvious. Any help would be appreciated.
>>
>
> Take a closer look at g_wham -h.  The option you're asking about is definitely
> there.  Also be sure you're using the version you think you are; g_wham was
> overhauled between 4.0.7 and 4.5.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

-- 
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---------------------------------------------------